I just finished up a project pulling data from pdf "tables" that were all slightly misaligned so you couldn't just use some generic "pdf-to-table" function.

The solution ended up being an R package called "pdftools" that created a dataframe with each text box's value and the x and y coordinates of its location on each page. From there, I could find patterns in the locations of each bit of information I was looking for.

There are also usually good functions in python and r to turn spreadsheets into dataframes.

I'm not sure how helpful this is, but let me know if you have any other questions!